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- EMDB-24709: Composite Map BORF2-APOBEC3Bctd Complex -

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Basic information

Entry
Database: EMDB / ID: EMD-24709
TitleComposite Map BORF2-APOBEC3Bctd Complex
Map dataComposite Map
Sample
  • Complex: BORFf2/APOBEC3Bctd
    • Complex: MBP-BORF2 (large subunit of EBV ribonucleotide reductase with n-terminal MBP tag)
      • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Ribonucleoside-diphosphate reductase large subunit
    • Complex: APOBEC3Bctd-mychis (human APOBEC3B protein with c-terminal mychis tag)
      • Protein or peptide: DNA dC->dU-editing enzyme APOBEC-3B
  • Ligand: ZINC ION
KeywordsHost-pathogen complex / viral protein / antiviral protein / deaminase / OXIDOREDUCTASE-HYDROLASE complex
Function / homology
Function and homology information


mRNA Editing: C to U Conversion / Formation of the Editosome / release from viral latency / single-stranded DNA cytosine deaminase / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / DNA cytosine deamination / cytidine to uridine editing / clearance of foreign intracellular DNA / cytidine deaminase activity / transposable element silencing ...mRNA Editing: C to U Conversion / Formation of the Editosome / release from viral latency / single-stranded DNA cytosine deaminase / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / DNA cytosine deamination / cytidine to uridine editing / clearance of foreign intracellular DNA / cytidine deaminase activity / transposable element silencing / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / P-body / outer membrane-bounded periplasmic space / defense response to virus / periplasmic space / DNA replication / innate immune response / DNA damage response / RNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus / membrane / cytoplasm
Similarity search - Function
Ribonucleotide reductase large subunit, Alphaherpesviruses / Novel AID APOBEC clade 2 / : / Ribonucleotide reductase, class I , alpha subunit / Ribonucleotide reductase large subunit signature. / Ribonucleoside-diphosphate reductase large subunit / Ribonucleotide reductase large subunit, N-terminal / Ribonucleotide reductase, all-alpha domain / Ribonucleotide reductase large subunit, C-terminal / Ribonucleotide reductase, barrel domain ...Ribonucleotide reductase large subunit, Alphaherpesviruses / Novel AID APOBEC clade 2 / : / Ribonucleotide reductase, class I , alpha subunit / Ribonucleotide reductase large subunit signature. / Ribonucleoside-diphosphate reductase large subunit / Ribonucleotide reductase large subunit, N-terminal / Ribonucleotide reductase, all-alpha domain / Ribonucleotide reductase large subunit, C-terminal / Ribonucleotide reductase, barrel domain / APOBEC/CMP deaminase, zinc-binding / Cytidine and deoxycytidylate deaminases zinc-binding region signature. / Cytidine and deoxycytidylate deaminase domain / Cytidine and deoxycytidylate deaminases domain profile. / Cytidine deaminase-like / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
Ribonucleoside-diphosphate reductase large subunit / Maltose/maltodextrin-binding periplasmic protein / DNA dC->dU-editing enzyme APOBEC-3B
Similarity search - Component
Biological speciesEpstein-Barr virus (Epstein-Barr virus) / Homo sapiens (human) / Human gammaherpesvirus 4 (Epstein-Barr virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.55 Å
AuthorsShaban NM / Yan R
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Sci Adv / Year: 2022
Title: Cryo-EM structure of the EBV ribonucleotide reductase BORF2 and mechanism of APOBEC3B inhibition.
Authors: Nadine M Shaban / Rui Yan / Ke Shi / Sofia N Moraes / Adam Z Cheng / Michael A Carpenter / Jason S McLellan / Zhiheng Yu / Reuben S Harris /
Abstract: Viruses use a plethora of mechanisms to evade immune responses. A recent example is neutralization of the nuclear DNA cytosine deaminase APOBEC3B by the Epstein-Barr virus (EBV) ribonucleotide ...Viruses use a plethora of mechanisms to evade immune responses. A recent example is neutralization of the nuclear DNA cytosine deaminase APOBEC3B by the Epstein-Barr virus (EBV) ribonucleotide reductase subunit BORF2. Cryo-EM studies of APOBEC3B-BORF2 complexes reveal a large >1000-Å binding surface composed of multiple structural elements from each protein, which effectively blocks the APOBEC3B active site from accessing single-stranded DNA substrates. Evolutionary optimization is suggested by unique insertions in BORF2 absent from other ribonucleotide reductases and preferential binding to APOBEC3B relative to the highly related APOBEC3A and APOBEC3G enzymes. A molecular understanding of this pathogen-host interaction has potential to inform the development of drugs that block the interaction and liberate the natural antiviral activity of APOBEC3B. In addition, given a role for APOBEC3B in cancer mutagenesis, it may also be possible for information from the interaction to be used to develop DNA deaminase inhibitors.
History
DepositionAug 19, 2021-
Header (metadata) releaseApr 27, 2022-
Map releaseApr 27, 2022-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_24709.png

Downloads & links

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Map

FileDownload / File: emd_24709.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite Map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.84 Å/pix.
x 336 pix.
= 283.584 Å		0.84 Å/pix.
x 336 pix.
= 283.584 Å		0.84 Å/pix.
x 336 pix.
= 283.584 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.844 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 10.0
Minimum - Maximum-3.075361 - 72.192539999999994
Average (Standard dev.)0.01320953 (±1.2892529)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 283.58398 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : BORFf2/APOBEC3Bctd

EntireName: BORFf2/APOBEC3Bctd
Components
  • Complex: BORFf2/APOBEC3Bctd
    • Complex: MBP-BORF2 (large subunit of EBV ribonucleotide reductase with n-terminal MBP tag)
      • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Ribonucleoside-diphosphate reductase large subunit
    • Complex: APOBEC3Bctd-mychis (human APOBEC3B protein with c-terminal mychis tag)
      • Protein or peptide: DNA dC->dU-editing enzyme APOBEC-3B
  • Ligand: ZINC ION

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Supramolecule #1: BORFf2/APOBEC3Bctd

SupramoleculeName: BORFf2/APOBEC3Bctd / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2

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Supramolecule #2: MBP-BORF2 (large subunit of EBV ribonucleotide reductase with n-t...

SupramoleculeName: MBP-BORF2 (large subunit of EBV ribonucleotide reductase with n-terminal MBP tag)
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Epstein-Barr virus (Epstein-Barr virus)

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Supramolecule #3: APOBEC3Bctd-mychis (human APOBEC3B protein with c-terminal mychis tag)

SupramoleculeName: APOBEC3Bctd-mychis (human APOBEC3B protein with c-terminal mychis tag)
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Maltose/maltodextrin-binding periplasmic protein,Ribonucleoside-d...

MacromoleculeName: Maltose/maltodextrin-binding periplasmic protein,Ribonucleoside-diphosphate reductase large subunit
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: ribonucleoside-diphosphate reductase
Source (natural)Organism: Human gammaherpesvirus 4 (Epstein-Barr virus)
Molecular weightTheoretical: 133.408031 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKIEEGKLVI WINGDKGYNG LAEVGKKFEK DTGIKVTVEH PDKLEEKFPQ VAATGDGPDI IFWAHDRFGG YAQSGLLAEI TPAAAFQDK LYPFTWDAVR YNGKLIAYPI AVEALSLIYN KDLLPNPPKT WEEIPALDKE LKAKGKSALM FNLQEPYFTW P LIAADGGY ...String:
MKIEEGKLVI WINGDKGYNG LAEVGKKFEK DTGIKVTVEH PDKLEEKFPQ VAATGDGPDI IFWAHDRFGG YAQSGLLAEI TPAAAFQDK LYPFTWDAVR YNGKLIAYPI AVEALSLIYN KDLLPNPPKT WEEIPALDKE LKAKGKSALM FNLQEPYFTW P LIAADGGY AFKYAAGKYD IKDVGVDNAG AKAGLTFLVD LIKNKHMNAD TDYSIAEAAF NKGETAMTIN GPWAWSNIDT SA VNYGVTV LPTFKGQPSK PFVGVLSAGI NAASPNKELA KEFLENYLLT DEGLEAVNKD KPLGAVALKS YEEELAKDPR IAA TMENAQ KGEIMPNIPQ MSAFWYAVRT AVINAASGRQ TVDAALAAAQ TNAAAMATTS HVEHELLSKL IDELKVKANS DPEA DVLAG RLLHRLKAES VTHTVAEYLE VFSDKFYDEE FFQMHRDELE TRVSAFAQSP AYERIVSSGY LSALRYYDTY LYVGR SGKQ ESVQHFYMRL AGFCASTTCL YAGLRAALQR ARPEIESDME VFDYYFEHLT SQTVCCSTPF MRFAGVENST LASCIL TTP DLSSEWDVTQ ALYRHLGRYL FQRAGVGVGV TGAGQDGKHI SLLMRMINSH VEYHNYGCKR PVSVAAYMEP WHSQIFK FL ETKLPENHER CPGIFTGLFV PELFFKLFRD TPWSDWYLFD PKDAGDLERL YGEEFEREYY RLVTAGKFCG RVSIKSLM F SIVNCAVKAG SPFILLKEAC NAHFWRDLQG EAMNAANLCA EVLQPSRKSV ATCNLANICL PRCLVNAPLA VRAQRADTQ GDELLLALPR LSVTLPGEGA VGDGFSLARL RDATQCATFV VACSILQGSP TYDSRDMASM GLGVQGLADV FADLGWQYTD PPSRSLNKE IFEHMYFTAL CTSSLIGLHT RKIFPGFKQS KYAGGWFHWH DWAGTDLSIP REIWSRLSER IVRDGLFNSQ F IALMPTSG CAQVTGCSDA FYPFYANAST KVTNKEEALR PNRSFWRHVR LDDREALNLV GGRVSCLPEA LRQRYLRFQT AF DYNQEDL IQMSRDRAPF VDQSQSHSLF LREEDAARAS TLANLLVRSY ELGLKTIMYY CRIEKAADLG VMECKASAAL SVP REEQNE RSPAEQMPPR PMEPAQVAGP VDIMSKGPGE GPGGWCVPGG LEVCYKYRQL FSEDDLLETD GFTERACESC Q

UniProtKB: Maltose/maltodextrin-binding periplasmic protein, Ribonucleoside-diphosphate reductase large subunit

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Macromolecule #2: DNA dC->dU-editing enzyme APOBEC-3B

MacromoleculeName: DNA dC->dU-editing enzyme APOBEC-3B / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: single-stranded DNA cytosine deaminase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.342541 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDPDTFTFNF NNDPLVLRRR QTYLCYEVER LDNGTWVLMD QHMGFLCNEA KNLLCGFYGR HAELRFLDLV PSLQLDPAQI YRVTWFISW SPCFSWGCAG EVRAFLQENT HVRLRIFAAR IYDYDPLYKE ALQMLRDAGA QVSIMTYDEF EYCWDTFVYR Q GCPFQPWD ...String:
MDPDTFTFNF NNDPLVLRRR QTYLCYEVER LDNGTWVLMD QHMGFLCNEA KNLLCGFYGR HAELRFLDLV PSLQLDPAQI YRVTWFISW SPCFSWGCAG EVRAFLQENT HVRLRIFAAR IYDYDPLYKE ALQMLRDAGA QVSIMTYDEF EYCWDTFVYR Q GCPFQPWD GLEEHSQALS GRLRAILQNQ GNKLGPEQKL ISEEDLNSAV DHHHHHH

UniProtKB: DNA dC->dU-editing enzyme APOBEC-3B

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.55 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 243192
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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